Module: SLiMDIP Description: Short Linear Motif-Domain Interaction Prediction Version: 0.1.0 Last Edit: 25/10/16

Copyright © 2015 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_obj rje_slimlist

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This program combines the outputs from several other programs to produce a filtered list of predicted SLiM-mediated interactions in which: - hub proteins contain a SLiM-binding domain - spoke proteins contain a predicted SLiM - PPI data supports an interaction between hub and spoke for matching SLiMs and SLiM-binding domains

SLiMDIP can be run in several different modes depending on the nature of the input data and the desired output.

SLiMDIP mode

The basic functionality of this program is a four-way join of data:
- A protein-protein interaction table linking hub proteins to spoke proteins.
- An occurrence table (generated by SLiMProb) linking SLiMs to Spoke protein sequences.
-

NOTE: For full functionality, hub proteins should have Uniprot identifiers (HubUni field). If seqin=FASFILE is not
given, spoke proteins should also have Uniprot identifiers (SpokeUni), else they should have identifiers in a
SpokeSeq field that match sequence names in the seqin=FASFILE file.

Legacy Mode

This mode needs all of the input files to pre-exist.

A gene field is generated from the Seq field in occfile (the first element, split on "_"), which is used to cross-
reference to the Hub field of the PPIFile.

Commandline

Main SLiMDIP Options

dipmode=X : Run mode for SLiMDip (slimdip/mimicry/enrichment/legacy) [slimdip]
basefile=FILE : Sets the basefile for all input/output. If not given, will use the ppifile=FILE base [None]
ppifile=PPIFILE : Pairwise PPI file with HubUni and SpokeUni or SpokeSeq fields. [BASEFILE.ppi.tdt]
seqin=FASFILE : File containing spoke protein sequences. If not found, will generate from SpokeUni field [None]
motifs=FILE : File containing the SLiMs to analyse. (Required.) "ELM" will create/use ELM download. [ELM]
dmifile=DSVFILE : File containing SLiMs and interacting Pfam domains. ['elm_interaction_domains.tsv']
uniprot=DATFILE : Source for PPI Hub Uniprot entries. Will create if missing. [uniprot]
domfile=DSVFILE : Protein-domain (Uniprot-Pfam) linkage file. Will create if missing. [None]
runid=X : RunID for SLiMProb run. (Can also extract from SLiMProb occ.csv file [SLiMDIP]

SLiM DMI Enrichment Options

randbase=X : This is the base of the randbase.X.tdt shuffled PPI files [BASEFILE.rand]
randppi=X : Number of random PPI datasets to generate for enrichment analysis [1000]
randmethod=X : Method for randomisation (shuffle/edgeswap) [shuffle]
edgeswap=X : Number of times to swap edges (x edge number) for edge swap method [10]

Legacy Input Options

occfile=DSVFILE : SLiM prediction (e.g. SLiMProb) occurrence file with Motif and Seq fields [None]
ppifile=PPIFILE : Pairwise PPI file with HubUni and SpokeUni fields [None]
domfile=DSVFILE : Protein-domain linkage file [None]
dmifile=DSVFILE : Delimited text file linking Motifs with Proteins via SLiM-interaction domains [None]

History Module Version History

    # 0.0.0 - Initial Compilation.